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A powerful member of the Indiana Board of Pharmacy was quietly involved in discussions with state pharmacy regulators about a $100 million project that benefited his employer — Walgreens pharmacies.

And now a government watchdog group and a labor federation say those actions not only violated state ethics laws, but have allowed Walgreen Co. to dramatically remodel dozens of stores across Indiana, compromising patient privacy and increasing the chance of errors in filling prescriptions.

One of the groups persuaded the U.S. Department of Health and Human Services to look into the matter. It recently launched an investigation into the patient privacy allegations at Walgreen.

Walgreen said it is cooperating with the investigation, and defended the store layout as safe and effective. “We presented this model to more than 30 boards of pharmacy around the country,” said Michael Polzin, a company spokesman in Illinois. “We’re very proud of the work we have done.”

In dozens of emails from 2011 reviewed by The Indianapolis Star, William J. Cover — then president of the state pharmacy board — played a key role in connecting state regulators with Walgreen officials months before the remodeling project became public.

During that time, Cover was corporate manager of pharmacy affairs for Walgreen — raising questions about whether he should have removed himself from any involvement with state officials concerning the project.

It seems clear he didn’t.

In one email, the executive director of the pharmacy board asked top state officials whether board members could travel to Illinois to visit Walgreen headquarters. “This is a specific request from my Board President,” wrote Phil Wickizer, referring to Cover.

In various emails spanning five months in 2011, Cover arranged two trips for the Board of Pharmacy to Walgreen sites in Illinois to meet company officials and inspect the new design. He sent information about the project to the Board of Pharmacy staff.

Walgreen was proposing a radical departure from most pharmacies, dubbed the “Well Experience.” The plan was to move pharmacists out from behind the counter to a workstation on the floor, where they could answer questions from the public and provide health counseling. Indiana was the pilot site.

Walgreen said it would spend about $100 million in infrastructure, hire 150 new employees and spend millions more in marketing and technology.

According to an email from Wickizer to the Indiana Professional Licensing Agency on May 11, 2011, “Walgreens wants to partner with the Board and get your buy-in before making such a commitment.” He said the company wanted to keep the plans confidential.

“I told them this would not be an issue,” Wickizer wrote.

The licensing association warned that the meeting in Chicago might violate Indiana’s open doors laws, and in a subsequent email, Wickizer reported to Walgreen officials that the board would go in two groups to avoid a quorum, which would require public notice.

Before the trips, Cover asked Wickizer whether other board members were supporting the project.

“Reaction so far?” Cover wrote on May 11, two months before the vote. Wickizer responded that three of the other six board members so far “have responded affirmatively.” An hour later, Cover followed up with Wickizer: “Thanks for all your hard work on this project. It is certainly appreciated.”

In an email three days before Walgreen’s project became public at a Board of Pharmacy meeting, Cover wrote to Wickizer: “Monday will be fun!!”

On Monday, July 11, 2011, Walgreen officials appeared before the board to explain the project. The board voted 6-0 to approve it, with Cover abstaining due to a conflict stemming from his employment at Walgreen.

Wickizer left Indiana government in 2012 to take a job as senior legal counsel at Express Scripts, a pharmaceutical mail-order operation based in St. Louis. He referred questions to the Indiana Professional Licensing Agency.

Cover, who is still on the board but no longer serves as president, did not return numerous phone calls to his office and home in Middlebury.

Sue Swayze, a spokeswoman for the Indiana Professional Licensing Agency, defended Cover’s conduct, saying he was merely coordinating logistical and scheduling issues, such as the trip to Chicago, while keeping himself out of substantive discussions of the project.

“We are sticklers about recusing ourselves from that discussion” when there are conflicts, she said.

She said it would be up to the state’s public access counselor or inspector general to making a legal ruling.

Two citizens groups say they plan to file a complaint Monday, with the Indiana inspector general’s office. Common Cause Indiana and Change to Win, a labor-supported activist group, say that Cover’s actions violated the Indiana ethics code. The emails were obtained by Change to Win under numerous open-records requests.

Julia Vaughn, director of Common Cause, a government watchdog group, said Cover should have removed himself completely from the matter.

“Under the circumstances, he should have kept himself at arm’s length,” she said. “Looking at the emails, I think more separation was needed, and that’s why we think an investigation is necessary.”

Change to Win said it has made more than 100 visits to Well Experience stores and has found widespread risks to patient privacy and public health. Pharmacists often leave their desks in a public area of the store to talk to patients in consulting rooms or to unlock a cabinet in the dispensing area.

When the pharmacist leaves, the public can look at the computer screens or at labeled bottles of medicine on their desk, the organization said. About 80 percent of the stores visited violated privacy laws in this way, the group alleged.

“No one wants to have their prescription for methadone or Viagra or their dependence on prescription painkillers sitting out on a desk for their neighbors or employees to see,” said Nell Geiser, an official with Change to Win in New York.

The watchdog groups say officials’ haste in approving the project may have caused them to inadvertently violate the Indiana pharmacy laws that existed at that time. Indiana law required pharmacists to provide “immediate and personal supervision” to other pharmacy staff. Two years later, in 2013, the Indiana pharmacy regulations were amended to allow certain types of remote supervision.

Polzin, the Walgreen spokesman, declined to comment on the allegations against Cover, except to say the company expects all its employees to follow all laws.